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Fig. 2 in Workflow of Lotmaria passim isolation: Experimental infection with a low-passage strain causes higher honeybee mortality rates than the PRA-403 reference strain
Fig. 2. Kaplan-Meier survival curves for the experimental groups (C1, control and PRA-403), showing the cumulative mortality over time. Vertical ticks indicate censored observations.
Fig. 1 in Workflow of Lotmaria passim isolation: Experimental infection with a low-passage strain causes higher honeybee mortality rates than the PRA-403 reference strain
Fig. 1. Workflow for the isolation of bee-infecting trypanosomatid parasites from honeybee guts. A. Dissection and tissue processing (steps 1–4), and trypanosomatid culture and expansion (step 5) in liquid or Solid Cultures. B. Growth curve of L. passim PRA-403 strain in decreasing concentrations of 5-Fluorocytosine (1 × 106 μg/ mL-100 μg/mL) to determine the maximum dose for parasite survival. C. Giemsa staining of L. passim C1 (CCP 1). D. Hoescht DNA staining of live L. passim C1 (CCP 1): N, Nucleus; K, Kinetoplast; E, Scanning Electron Microscopy of L. passim C1 (CCP 1) grown in Agar Solid cultures 20 days post-inoculation.
TRcompDB v1.0, a global reference of tandem repeat variation
<p>The v-2.1 "vamos" motif sets and the TR annotations using 360 publicly available long-read assemblies (TRCompDB).Data are provided for both GRCh38 and T2T-CHRM13 reference genomes. TR annotations are provided as combined vcf file. “oriMotifs” stands for the full motif set before efficient motif selection. “effMotifs-0.x” stands for the efficient motifs selected under q=0.x.</p>
FIGURE 3. 3.1 von Mises stresses, 3.2 von Mises strains, 3.3 Displacements, 3.4 von Mises stress relationship with reference value, 3.5 von Mises strain relationship with reference value and 3.6 in Insights into the controversy over materials data for the comparison of biomechanical performance in vertebrate
FIGURE 3. 3.1 von Mises stresses, 3.2 von Mises strains, 3.3 Displacements, 3.4 von Mises stress relationship with reference value, 3.5 von Mises strain relationship with reference value and 3.6 Displacement relationship with reference value in front of variation in the elastic modulus (E) in points P and Q.
FIGURE 5. 5.1 von Mises stresses, 5.2 von Mises strains, 5.3 Displacements, 5.4 von Mises stress relationship with reference value, 5.5 von Mises strain relationship with reference value and 5.6 in Insights into the controversy over materials data for the comparison of biomechanical performance in vertebrate
FIGURE 5. 5.1 von Mises stresses, 5.2 von Mises strains, 5.3 Displacements, 5.4 von Mises stress relationship with reference value, 5.5 von Mises strain relationship with reference value and 5.6 Displacement relationship with reference value in front of variation in the elastic modulus (E) in points P and Q.
D-PLACE dataset derived from Binford 2001 'Constructing Frames of Reference'
<p>Cite the source of the dataset as:</p> <blockquote> <p>Binford, L. 2001. Constructing Frames of Reference: An Analytical Method for Archaeological Theory Building Using Hunter-gatherer and Environmental Data Sets. University of California Press</p> </blockquote>
Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_34_SOP - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
UNITE+INSD 2024 Fungal ITS, ITS1, and ITS2 Reference Sequences and classification
<p>These datasets were created from the 2024 release (Abarenkov et al. 2024) of the UNITE+INSD database as reference sequences for and by dnabarcoder (Vu et al. 2022). The ITS1 and ITS2 sequences were extracted using ITSx (Bengtsson-Palme et al. 2013).</p>
Reference collection of combat wear traces on replicas of Bronze Age spears
<p>This Dataset comprises a collection of photographs of combat wear traces produced during various experiments focusing on the use of bronze spears in combat experiments as described in the paper <em>Gentile V., van Dijk C.J., ter Mors O., (2024): Multi-stage experiments in Bronze Age spear combat: insights on wear </em><em>formation, trauma, and combat contexts. Journal of Archaeological science (<a href="https://doi.org/10.1016/j.jas.2024.106044">https://doi.org/10.1016/j.jas.2024.106044</a></em><em>).</em> <br><br>Please read the README file for information on how to navigate the dataset. <br><br>This dataset is distributed under CC BY-NC 4.0 license: <a href="https://creativecommons.org/licenses/by-nc/4.0/">https://creativecommons.org/licenses/by-nc/4.0/ </a><br>For other uses, please contact the creator.</p> <p> </p>
FVLLMONTI Application examples: Single reconfigurable VNWFET TCAD simulation and Reference logic cell DTCO flow
<p>This data set presents two application examples collecting and highlighting some of the key components to the TCAD, compact modelling and DTCO approaches carried out as part of the FVLLMONTI project in relation to Deliverable D3.2.</p> <p>First we present an example that demonstrates the functionality of the U-shaped reconfigurable transistor, switching the device behaviour between NMOS and PMOS using the Program Gate and giving the transistor characteristics of those devices.</p> <p>Secondly, this data set gives an introduction into the FVLLMONTI DTCO approach. The provided simulation project shows a reference DTCO flow from layout to library characteristics for previously delivered physical logic cell designs. The DTCO flow provides insight into logic cell parasitics, netlist for 3rd party SPICE analysis, and KPI determination and characterization.</p> <p>Both simulation projects can be seen as template for similar setups employed to overcome the challenges and answer the detailed questions faced in investigating a newly developed semiconductor technology such as the FVLLMONTI stack.</p>
A tectonic-rules-based mantle reference frame since 1 billion years ago – implications for supercontinent cycles and plate–mantle system evolution
<p>The archive <strong>Muller_etal_2022_SE_1Ga_Opt_PlateMotionModel.zip</strong> contains the files for the plate model in an optimised mantle reference frame. GPlates or pyGPlates software (<a href="https://www.gplates.org/">www.gplates.org</a>) is needed to read these files. </p> <p>The archive <strong>Muller_etal_2022_SE_mantle-ref-frame-oceanic-crustal-agegrids.zip</strong> contains the oceanic crustal age grids in netCDF-4 format for the optimised mantle reference frame plate model, while the archive <strong>Muller_etal_2022_SE_PMAG_oceanic-crustal-agegrids.zip</strong> contains the oceanic crustal age grids in netCDF-4 format for the paleomagnetic reference frame plate model from Merdith et al. (2021).</p> <p> </p> <p>The agegrids associated with this model can be accessed at: <a href="https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Muller_etal_2022_SE/" target="_blank" rel="noopener">https://repo.gplates.org/webdav/PlateModel_Age_SR_Grids/Muller_etal_2022_SE/</a></p>
Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards
<h1>Lab_33_OTHER - Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards - mzML files</h1><p>This dataset is part of the <a href="https://doi.org/10.5281/zenodo.12632989" target="_blank">ILS Ceramide Ring Trial</a>. The suffix 'SOP' indicates that the results were obtained using the recommended and standard operating procedure protocol to prepare and measure all samples, while the suffix 'OTHER' indicates that the corresponding lab prepared and measured the samples according to their own internal protocol. Please check the corresponding mapping file 'ILS-Ceramide-Ring-Trial-Datasets.csv' in the ILS Ceramide Ring Trial record for a mapping of the originally submitted lab reports and the final lab number as reported in the manuscript.</p><p>All reports together with the code for analysis and visualization, reproducing the figures in the manuscript, are available under the following doi: <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">https://zenodo.org/doi/10.5281/zenodo.10081970</a>. This links to releases of the following GitHub repository: <a href="https://github.com/lifs-tools/ils-ceramide-ring-trial" target="_blank">https://github.com/lifs-tools/ils-ceramide-ring-trial</a>. The archived version of the lab reports, workflow source code and manuscript visualizations are also available <a href="https://zenodo.org/doi/10.5281/zenodo.10081970" target="_blank">here</a>.</p><p>Please note that most datasets have been acquired in MRM mode, such that the msconvert conversion to mzML has stored the MRM data in the chromatogram part of the mzML files.</p> <p>The msconvert Docker container (Proteowizard release: 3.0.24172 (63d00b1), build date Jun 202 2024 20:01:14) was used with the native vendor libraries / peak picking for conversion, using default arguments. m/z values were encoded with 64 bit (default), while intensity values were encoded with 32 bit (default). All binary data was zlib-compressed.</p>
Fig. 10. Reference specimens from Laurussia. A. Diclitodus scitulus Davis, 1883 in Chondrichthyan remains from the Lower Carboniferous of Muhua, southern China
Fig. 10. Reference specimens from Laurussia. A. Diclitodus scitulus Davis, 1883, holotype (BMNH P.49629), from the Carboniferous Limestone, Richmond, Yorkshire, England, in labial view. B. "?Psephodus laevissimus", specimen BMNH P.9914, from the Lower Limestone shales bone bed, Avon Gorge near Bristol, in oral view. C. Chomatodus davisi (Woodward, 1889), a specimen of the type series (BMNH P.2656), from the Viséan Mountain Limestone of Armagh, Northern Ireland, in lingual view. D. Tamiobatis wachsmuthi (St. John and Worthen, 1875), a specimen of the type series (MCZ 6371), from the Kinderhookian of Burlington, Iowa, in labial view. E. Deltodus sublaevis (Agassiz, 1838), specimen BGS 5964, from the Viséan Mountain Limestone of Armagh, Northern Ireland, in oral view (left side broken). F.?Goodrichthys eskdalensis (Moy−Thomas, 1936), a tooth from the specimen NMS 2000.14.2, from the lower Viséan of Glencartholm, Dumfriesshire, Scotland, in labial view. G. Chomatodus linearis (Agassiz, 1838), specimen BMNH P.2653, from the Lower Carboniferous Yoredale Beds, Richmond, Yorkshire, England, in oral view. H. Sibyrhynchus denisoni Zangerl and Case, 1973 (FMNH PF6408), palatal tooth plates.
Structure and Excitation Spectra of Third-Row Transition Metal Hexafluorides Based on Multi-Reference Exact Two-Component Theory: Dataset
<p>This dataset collects the unprocessed (= outputs from calculations) results discussed in the paper titled "Structure and Excitation Spectra of Third-Row Transition Metal Hexafluorides Based on Multi-Reference Exact Two-Component Theory", by Ayaki Sunaga.</p>
Arab Pangenome Reference
<p>Pangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phased <em>de novo</em> assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.</p>
Data from multi-sensor devices and reference station to monitoring urban air quality
<p>Data from electrochemical and optical sensors.</p> <h3>Files names</h3> <ul> <li>ECT01, ECT02, ECT06, ECT07 = device name</li> <li>ISSEP = reference station <ul> <li>"c" = calibration data</li> <li>"v" = validation data</li> </ul> </li> </ul> <h3>Variable description</h3> <table> <tbody> <tr> <td><strong>Electrochemical sensor</strong></td> <td><strong>Optical sensor</strong></td> <td><strong>Probe</strong></td> <td><strong>Reference</strong></td> </tr> <tr> <td> <p>AE = auxiliary electrode (mV)</p> <p>WE = working electrode (mV)</p> <p>N = temperature correction </p> <ul> <li>ch0 = CO sensor</li> <li>ch1 = OX sensor</li> <li>ch2 = NO2 sensor</li> <li>ch3 = NO sensor</li> </ul> </td> <td> <p>PM1, PM2.5 and PM10 in µg/m³</p> </td> <td> <p>Prs_mbar = pressure (mbar)</p> <p>Temp = temperature (°C)</p> <p>RH = relative humidity (%)</p> </td> <td> <p>DV30 = wind direction @ 30m (°)</p> <p>HR = relative humidity (%)</p> <p>NO, NO2, O3, PM10 and PM2.5 (µg/m³)</p> <p>Precipita = precipitation (mm)</p> <p>TC3 = temperature @ 3m (°C)</p> <p>VV30 = wind speed @ 30m (m/s)</p> </td> </tr> </tbody> </table> <p> </p>
Tabl. 2 in The Jordan theropod (Maastrichtian, Montana, U. S. A.) referred to the genus Aublysodon
<p>Tabl. 2 - Characters used in determining the relationships of Aublysodon. Caractères utilises pour determiner la position systématique Ae Aublysodon.</p><table><tbody><tr><th>character</th><th>plesiomorphic/apomorphic</th></tr></tbody><tbody><tr><th>1. premaxillary teeth D-shaped in section</th><td>a</td></tr><tr><th>2. premaxillary teeth not serrate</th><td>p</td></tr><tr><th>3. premaxillary teeth with low ridge on posterior face</th><td>a</td></tr><tr><th>4. cheek teeth relatively large (with respect to depthof muzzle and jaw)</th><td>p</td></tr><tr><th>5. muzzle long and low</th><td>p</td></tr><tr><th>6. frontals longer than wide</th><td>p</td></tr><tr><th>7. two or three prongs of nasal overlap frontal</th><td>a</td></tr><tr><th>8. dorsolaterally directed prefrontal contact on frontal</th><td>p</td></tr><tr><th>9. socket for prefrontal on frontal</th><td>p</td></tr><tr><th>10. elongate contact for prefrontal on frontal</th><td>p</td></tr><tr><th>11. orbital rim on frontal very short</th><td>p</td></tr><tr><th>12. frontal-prefrontal suture expanded</th><td>p</td></tr><tr><th>13. pronounced buttress at frontal-postorbital contact</th><td>p</td></tr><tr><th>14. parietal process separates frontal posteriorly</th><td>p</td></tr><tr><th>15. sagittal crest extends onto frontals</th><td>p</td></tr><tr><th>16. frontals essentially flat between orbits</th><td>p</td></tr><tr><th>17. nasals smooth</th><td>p</td></tr><tr><th>18. anterior margin of antorbital fossa v-shaped</th><td>p</td></tr><tr><th>19. acute angle of premaxillary-maxillary contact withventral margin of snout</th><td>p</td></tr><tr><th>20. ventral margin of symphysis only slightly inclinedto horizontal</th><td>p</td></tr></tbody></table><p>Characters 1 to 8, 10, and 17 to 20 discussed in text, characters 9 and 11 to 16 from Currie (1987).</p>
BFR2: a curated benthic foraminifera ribosomal reference database
<p>The present data set provides a fasta file, a tab-separated text file, and an Excel file. The fasta file includes 5,324 18S rDNA reference sequences for benthic foraminifera. The tab-separated text file includes the following fields: BFR2 number = unique internal sequence accession number; length = sequence length; class = class to which each sequence is assigned; order/suborder/clade = order/suborder/clade to which each sequence is assigned; family = family to which each sequence is assigned; genus = genus to which each sequence is assigned; species = species to which each sequence is assigned; isolate number = unique DNA extraction number; clone/direct: indicates whether it has been directly sequenced or cloned; genbank_accession = NCBI sequence accession number; sampling site = biogeographic region where the specimen has been collected; latitude in decimal degrees, longitude in decimal degrees; collection date = year in which specimen was collected; collector = person who collected the specimen; publication = publication associated to the sequence; journal = journal associated to publication; first author = first author associated to publication/sequence; taxonomic remarks = additional taxonomic information/comment; sampling remarks = addional sampling information/comment.<br><br>List of added or updated:<br>- Clone/direct: indicates whether it has been directly sequenced or cloned.<br>- Latitude and longitude in decimal degrees.<br>- Genbank accession number of 1700 18S rRNA sequences added.</p>
Linked collectors and determiners for: Database on reference specimens for medicinal plants of the Meliaceae family, conserved at the CNARP herbarium.
Natural history specimen data linked to collectors and determiners held within, "Database on reference specimens for medicinal plants of the Meliaceae family, conserved at the CNARP herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514">https://bionomia.net/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514">https://gbif.org/dataset/f0ad347c-dfaf-4326-9bb3-5e25f9b45514</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Database on reference specimens for medicinal plants of the Rubiaceae family, conserved at the CNARP herbarium.
Natural history specimen data linked to collectors and determiners held within, "Database on reference specimens for medicinal plants of the Rubiaceae family, conserved at the CNARP herbarium". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c3caca74-616b-4bad-b795-b13adff022de">https://bionomia.net/dataset/c3caca74-616b-4bad-b795-b13adff022de</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c3caca74-616b-4bad-b795-b13adff022de">https://gbif.org/dataset/c3caca74-616b-4bad-b795-b13adff022de</a>. Formatted as a Frictionless Data package.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.